ProCKSI

= External Software for ProCKSI =
(needs to be updated)

Generate the following directories on each compute node to contain important executables:
{{{
/usr/local/procksi/CE/
/usr/local/procksi/Cluster/
/usr/local/procksi/DaliLite
/usr/local/procksi/FAST/
/usr/local/procksi/MaxCMO-MSVNS/
/usr/local/procksi/MolScript/
/usr/local/procksi/ROCCH/
/usr/local/procksi/TMalign/
/usr/local/procksi/URMS/
/usr/local/procksi/Vorolign/
/usr/local/procksi/SCOP/
}}}

For the following installation of the ProCKSI server components, the following executables must be present:
{{{
/usr/local/procksi/CE/CE
/usr/local/procksi/Cluster/qclust
/usr/local/procksi/DaliLite/DaliLite
/usr/local/procksi/FAST/fast
/usr/local/procksi/MaxCMO-MSVNS/MaxCMO-MSVNS
/usr/local/procksi/MolScript/molscript
/usr/local/procksi/MolScript/molauto
/usr/local/procksi/ROCCH/ROCCH
/usr/local/procksi/TMalign/TMalign
/usr/local/procksi/URMS/urms
/usr/local/procksi/Vorolign/vorolign.jar
}}}

The following SCOP databases must present:
{{{
/usr/local/procksi/SCOP/dir.cla.scop.txt
/usr/local/procksi/SCOP/dir.cla.scop.txt_UniqueMulti
/usr/local/procksi/SCOP/dir.cla.scop.txt_UniqueSkip
}}}

== Image Software ==

=== !MolScript ===
* Download ''!MolScript'' from the repository.
* Make sure that the ''freeglut'' and ''freeglut-devel'' packages are installed.
* Compile using the Makefile provided for the x32- or x64-architecture.

!MolScript needs an X display in order to generate images (jpg, gif, …). Its possible to use the console X display for the OpenGL bits even if it is not logged in. Therefore, ''procksi'' must be authenticated and allowed to use this X display virtually.

Get and unpack the ProCKSI x-authentication patch from [repos:Externals/Cluster/xauth.tgz].

On each node copy magic cookie file for x-authentication:
{{{
cp :0.Xauth /var/gdm/:0.Xauth
}}}

On each node copy scripts for automatic x-authentication:
{{{
cp procksixauth /usr/local/sbin/procksixauth
cp :0 /etc/gdm/Init/:0
}}}

Restart the X display manager for the changes to take effect:
{{{
/usr/sbin/gdm-restart
}}}

The virtual X display can be used with unix socket '':0'', e.g.:
{{{
molauto protein.pdb | DISPLAY=unix:0.0 molscript -jpeg -out protein.jpeg
}}}

=== Other Visualisation Software ===
* Install ''!ImageMagick'' from the [source:Externals/Graphics repository] (sources) if not already installed
* Install ''Raster3D'' from the [source:Externals/Graphics repository] (sources)
* Install ''!GraphViz'' from the [source:Externals/Graphics repository] (RPM)
* Install ''pyparsing'' from the [source:Externals/Python repository] (sources)
* Install ''pydot'' from the [source:Externals/Python repository] (sources)